If you installed the F-5 in the SF2 Europe folder, then you will NOT have the F-5 when you launch the main SF2 (or SF2: Vietnam or SF2: Isreal). You will get the NATO mod and the F-5 ONLY if you use SF2 Europe.
However, you can launch all of the campaigns and missions from within SF2 Europe. So, in your case, if you wanted to fly an interception mission using an F-5 over Vietnam, you would still use the SF2 Europe launcher. Each individual .exe file contains all of the stock campaigns, planes and missions.
There isn't one main folder that applies to every launcher. Each launcher has its own folder. You can put all of your mods and custom controls into just the SF2 Europe folder and as long as you use the SF2 Europe launcher, then you will be able to use all of your mods in all of the stock terrains.
In my case (using Vista), I put all of my modded airplanes in (user)\Saved Games\ThirdWire\StrikeFighters2\Objects. If I want to fly an F-18 over Europe, I still use the Strike Fighters2.exe. Even f I want to fly A-4s for Isreal, I use the StrikeFighters2.exe. If I use anything but the SF2 launcher, I do not have access to any mods.
For you, just put all of your mods into the \StrikeFighters2 Europe\ appropriate folders and then launch the game using the Strike Fighters 2 Europe launcher regardless of the terrain or campaign you wish to run.
The other .exe files - and the related folders - are there for you to run different mods in different folders without having them conflicting with each other. If you wanted to use the Air/Ground Gold Expansion for Vietnam but didn't want any conflicts with your current NATO Fighters Mod, then you would have to use a different folder (e.g. SF2: Vietnam's folder). Then when running NATO fighters, you would use SF2: Europe. When you wanted to run A/G Gold you would run SF2: Vietnam. You would not have access to both mods simultaneously.